20180227_SH1_aliphaticsSRM

Start up functions

Read and organize data

read_srm_export <- function(filename, columns = c("peak_name", "RT.min", "basepeak", "area.cpm", "height.cts", "quantitation")) {
  filename %>% 
    # read excel files
    read_excel(sheet = "Integration", skip = 42, 
               col_names = columns, col_types = rep("text", length(columns))) %>% 
    as_data_frame() %>%
    # remove empty rows
    filter(!is.na(peak_name), peak_name != "n.a.") %>% 
    # convert the relevant numeric columns into numbers
    mutate_at(vars(RT.min, area.cpm, height.cts), as.numeric) %>% 
    # remove useless columns
    select(-basepeak, -quantitation) %>% 
    # add filename info
    mutate(file_id = gsub("\\.xls", "", basename(filename))) %>% 
    select(file_id, everything())
}

# get data
all_data <- 
  # find all excel files ##change name and use new folder for new project
  list.files("data_SH1", recursive = TRUE, full.names = TRUE, pattern = "\\.xls$") %>% 
  # send them to the read method
  lapply(read_srm_export) %>% 
  # combine the data set
  bind_rows() %>% 
  # pull out sample information
  #mutate(sample_id = str_match(all_data$file_id, "TSQ\\d+_GB_(.*)$") %>% { .[,2] }) %>% 
  # get n replicates
  group_by(file_id)
  #mutate(n_replicates = length(unique(file_id)))

File names for metadata file

Plot to check the spread

by sequence

all_data %>% 
  ggplot() + 
  aes(x = peak_name, y = area.cpm, color = file_id) +
  geom_point(size = 3) +
  theme_bw() +
  theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust = 1))

##by sample

all_data %>% 
  ggplot() +
  aes(x = file_id, y = area.cpm, color = file_id) + 
  geom_point(size = 3) +
  facet_wrap(~peak_name, scales = "free_y") +
    theme_bw() +
  theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust = 1),
        legend.position = "none")

Calculation peak amounts and rock concentrations, ID standards

depth_and_rock_info <- read_excel(file.path("metadata", "aliphaticSRM_SH1.xlsx")) %>% 
  rename(tle = `TLE.mg`, maltene = `maltenes.mg`, ref_amount_added.ug = `D4.ug` )%>% 
  filter(!is.na(file_id))
kable(depth_and_rock_info)

file_id	OG	depth	rock.g	tle	maltene	ref_amount_added.ug
TSQ3481_GB_OG002	2	125.015	10.001	24.9	13.7	100
TSQ3482_GB_OG003	3	124.000	10.120	224.4	7.3	100
TSQ3483_GB_OG004	4	123.000	10.320	-14.4	5.0	100
TSQ3484_GB_OG005 (50_)	5	122.000	9.280	3.2	5.4	100
TSQ3485_GB_OG006	6	121.000	10.624	33.4	NA	100
TSQ3486_GB_OG007	7	119.000	9.620	-214.2	4.8	100
TSQ3489_GB_OG008	8	118.000	9.698	3.4	5.0	100
TSQ3490_GB_OG009	9	117.010	10.742	5.0	6.3	100
TSQ3491_GB_OG010	10	115.000	11.070	5.0	6.0	100
TSQ3492_GB_OG011	11	114.000	10.208	0.4	6.9	100
TSQ3495_GB_OG012	12	113.000	10.552	9.4	11.4	100
TSQ3496_GB_OG013	13	111.080	9.747	6.9	9.5	100
TSQ3497_GB_OG014 (25_)	14	110.100	10.273	14.5	14.0	100
TSQ3498_GB_OG015	15	109.100	10.984	13.3	15.3	100
TSQ3477_GB_OG016	16	108.300	10.089	5.1	NA	100
TSQ3499_GB_OG017	17	106.900	10.348	-6.2	6.8	100
TSQ3476_GB_OG018	18	106.090	10.337	4.9	6.5	100
TSQ3473_GB_OG019	19	105.100	11.002	2.2	-5.2	100
TSQ3474_GB_OG020	20	104.090	10.911	5.6	7.2	100
TSQ3475_GB_OG021	21	102.890	10.056	21.6	7.4	100
TSQ3466_GB_OG022	22	101.900	11.025	4.5	7.2	100
TSQ3467_GB_OG023	23	101.100	11.294	8.5	NA	100
TSQ3468_GB_OG025	25	98.900	10.713	7.8	8.6	100
TSQ3469_GB_OG026	26	98.090	9.336	4.7	7.4	100
TSQ3472_GB_OG027	27	96.890	9.378	5.3	6.3	100
TSQ3503_GB_OG028	28	96.090	9.758	6.9	7.3	100
TSQ3504_GB_OG029	29	95.080	11.469	4.3	2.3	100
TSQ3505_GB_OG030	30	94.560	10.195	7.1	8.2	100
TSQ3506_GB_OG031	31	119.950	7.502	2.6	4.7	100
TSQ3507_GB_OG032	32	115.885	9.032	-2.1	4.4	100
TSQ3508_GB_OG033	33	112.070	7.287	2.3	-7.2	100
TSQ3511_GB_OG037	37	121.600	10.534	5.2	3.6	100
TSQ3512_GB_OG038	38	120.700	11.444	3.3	2.2	100
TSQ3513_GB_OG039	39	120.100	7.997	0.8	0.9	100
TSQ3514_GB_OG041	41	120.405	11.393	2.3	1.9	100
TSQ3515_GB_OG042	42	NA	NA	NA	NA	100
TSQ3516_GB_OG043	43	122.900	11.349	14.7	11.9	100
TSQ3519_GB_OG044	44	120.300	11.390	3.5	2.7	100
TSQ3520_GB_OG045	45	120.205	10.757	4.1	2.4	100
TSQ3521_GB_OG046	46	121.500	11.191	24.7	3.1	100
TSQ3522_GB_OG047 (50_)	47	121.105	10.868	38.8	5.5	100
TSQ3523_GB_OG049	49	122.600	11.260	30.0	12.7	100
TSQ3524_GB_OG050 (50_)	50	120.600	11.195	16.1	2.1	100
TSQ3527_GB_OG051	51	120.900	14.166	96.8	6.3	100
TSQ3528_GB_OG052	52	121.800	10.268	4.5	3.0	100
TSQ3529_GB_OG053	53	122.805	10.786	71.2	6.7	100
TSQ3530_GB_OG054	54	122.700	12.054	77.3	13.5	100
TSQ3531_GB_OG056	56	121.700	11.024	22.8	3.0	100
TSQ3532_GB_OG057	57	122.500	10.939	36.8	12.6	100
TSQ3535_GB_OG058	58	121.195	10.711	18.4	4.2	100
TSQ3536_GB_OG059	59	122.090	9.486	54.9	3.6	100
TSQ3537_GB_OG060	60	122.200	11.367	53.3	2.8	100
TSQ3538_GB_OG061	61	121.400	12.044	40.7	4.0	100
TSQ3539_GB_OG062	62	120.950	10.341	83.1	7.8	100
TSQ3540_GB_OG063	63	122.390	10.116	139.5	8.8	100
TSQ3541_GB_OG064	64	122.305	10.957	42.9	2.2	100
TSQ3544_GB_OG065	65	107.900	10.694	40.0	5.3	100
TSQ3634_GB_OG153	153	116.810	11.177	9.8	3.9	100
TSQ3635_GB_OG154	154	116.600	12.080	29.1	3.6	100
TSQ3636_GB_OG155	155	119.850	11.042	7.1	1.6	100
TSQ3637_GB_OG156	156	117.400	11.244	8.0	3.3	100
TSQ3638_GB_OG157	157	118.800	11.346	8.3	2.6	100
TSQ3639_GB_OG158	158	119.550	11.853	7.6	3.2	100
TSQ3647_GB_OG159	159	119.655	11.044	6.7	3.8	100
TSQ3648_GB_OG160	160	118.300	11.305	7.4	2.1	100
TSQ3649_GB_OG161	161	116.490	10.770	8.4	2.9	100
TSQ3650_GB_OG162	162	116.900	10.931	10.9	4.1	100
TSQ3654_GB_OG164	164	118.100	10.619	7.6	3.5	100
TSQ3655_GB_OG165	165	119.570	11.300	5.0	1.6	100
TSQ3656_GB_OG166	166	118.600	10.790	7.1	1.9	100
TSQ3657_GB_OG167	167	117.490	10.853	8.8	2.9	100
TSQ3658_GB_OG168	168	118.965	11.259	6.3	2.0	100

data_by_depth <- 
  all_data %>%
  left_join(depth_and_rock_info, by = "file_id") %>% 
  group_by(file_id) %>% 
  mutate(
    n_peaks = n(),
    n_standards = sum(peak_name == "D4 C29 ISTD"),
    ref_area.cpm = area.cpm[peak_name == "D4 C29 ISTD"],
    amount.ug = area.cpm/ref_area.cpm * ref_amount_added.ug,
    
     ##Normalize by what you want!
    conc_rock.ug_g = amount.ug / rock.g, 
    conc_tle.ug.g = amount.ug / tle,  
    conc_maltene.ug.g = amount.ug / maltene
    
  )%>% ungroup() %>% 
  arrange(file_id, peak_name) 
###if this does not run, it's likely due to a problematic sample (i.e. did not inject). check that all samples used here indeed have both standards present and properly integrated.

data_by_depth

## # A tibble: 10,126 x 18
##    file_id  peak_name  RT.min area.cpm height.cts    OG depth rock.g   tle
##    <chr>    <chr>       <dbl>    <dbl>      <dbl> <dbl> <dbl>  <dbl> <dbl>
##  1 TSQ3466… 20R 4a,24…   34.7    44365     400048  22.0   102   11.0  4.50
##  2 TSQ3466… 20R, 4a M…   33.4    33268     424790  22.0   102   11.0  4.50
##  3 TSQ3466… 20R, 4a M…   32.8    48349     759077  22.0   102   11.0  4.50
##  4 TSQ3466… 20S, 4a M…   32.1    48728     879884  22.0   102   11.0  4.50
##  5 TSQ3466… 20S, 4a,2…   35.8    30909     259440  22.0   102   11.0  4.50
##  6 TSQ3466… 20S, 4a,2…   34.0    46342     445181  22.0   102   11.0  4.50
##  7 TSQ3466… 25-nor C2…   37.6    11915     155542  22.0   102   11.0  4.50
##  8 TSQ3466… 28, 30 C2…   37.0    27634     343969  22.0   102   11.0  4.50
##  9 TSQ3466… 29, 30 C2…   35.8     5411      63017  22.0   102   11.0  4.50
## 10 TSQ3466… 2RS, 4a,2…   35.3    24416     396212  22.0   102   11.0  4.50
## # ... with 10,116 more rows, and 9 more variables: maltene <dbl>,
## #   ref_amount_added.ug <dbl>, n_peaks <int>, n_standards <int>,
## #   ref_area.cpm <dbl>, amount.ug <dbl>, conc_rock.ug_g <dbl>,
## #   conc_tle.ug.g <dbl>, conc_maltene.ug.g <dbl>

Calculate Recovery

Linear regressions of the calibration curves

standard <- read_excel(file.path("metadata", "D4_calibration.xlsx"))   ###read excel

###calibration curve
standard %>% 
  ggplot() +
  aes(x = Known.ng, y = Measured_area.counts, color = calibration) + 
  geom_smooth(method = "lm", alpha = 0.5) +
  geom_point() +
  theme_bw() +
  theme(legend.position = "none") 

calibrations <- 
  standard %>% 
  filter(!is.na(calibration)) %>% 
  nest(-calibration) %>% 
  mutate(
    fit = map(data, ~summary(lm(`Measured_area.counts`~ `Known.ng`, data = .x))),
    coefficients = map(fit, "coefficients"),
    intercept = map_dbl(coefficients, `[`, 1, 1),
    intercept_se = map_dbl(coefficients, `[`, 1, 2),
    slope = map_dbl(coefficients, `[`, 2, 1),
    slope_se = map_dbl(coefficients, `[`, 2, 2),
    r2 = map_dbl(fit, "r.squared")
  )

calibrations

## # A tibble: 1 x 9
##   calibration data      fit      coefficients intercept intercept_se slope
##   <chr>       <list>    <list>   <list>           <dbl>        <dbl> <dbl>
## 1 jan2018     <tibble … <S3: su… <dbl [2 × 4…       706         1371 72930
## # ... with 2 more variables: slope_se <dbl>, r2 <dbl>

calibrations %>% select(-data, -fit, -coefficients) %>% knitr::kable(d = 3)

calibration	intercept	intercept_se	slope	slope_se	r2
jan2018	705.862	1371.146	72929.67	3337.256	0.996

Determine yield

These numbers are not useful for anything else.

calib_data <-
  data_by_depth %>% 
  # temp
  mutate(calibration = "jan2018") %>% 
  left_join(calibrations, by = "calibration") %>% 
  mutate(
    total_volume.uL = 100,
    total_inject.uL = 1.5,
    ref_amount_inject_expected.ng = (ref_amount_added.ug * 1000)/total_volume.uL * total_inject.uL ,
    ref_amount_inject_measured.ng = (ref_area.cpm - intercept)/slope,
    ref_amount_measured.ug = ((total_volume.uL* ref_amount_inject_measured.ng)/total_inject.uL) * 1/1000,
    yield = (ref_amount_inject_measured.ng/ref_amount_inject_expected.ng) * 100
  )
  
calib_data

## # A tibble: 10,126 x 33
##    file_id  peak_name  RT.min area.cpm height.cts    OG depth rock.g   tle
##    <chr>    <chr>       <dbl>    <dbl>      <dbl> <dbl> <dbl>  <dbl> <dbl>
##  1 TSQ3466… 20R 4a,24…   34.7    44365     400048  22.0   102   11.0  4.50
##  2 TSQ3466… 20R, 4a M…   33.4    33268     424790  22.0   102   11.0  4.50
##  3 TSQ3466… 20R, 4a M…   32.8    48349     759077  22.0   102   11.0  4.50
##  4 TSQ3466… 20S, 4a M…   32.1    48728     879884  22.0   102   11.0  4.50
##  5 TSQ3466… 20S, 4a,2…   35.8    30909     259440  22.0   102   11.0  4.50
##  6 TSQ3466… 20S, 4a,2…   34.0    46342     445181  22.0   102   11.0  4.50
##  7 TSQ3466… 25-nor C2…   37.6    11915     155542  22.0   102   11.0  4.50
##  8 TSQ3466… 28, 30 C2…   37.0    27634     343969  22.0   102   11.0  4.50
##  9 TSQ3466… 29, 30 C2…   35.8     5411      63017  22.0   102   11.0  4.50
## 10 TSQ3466… 2RS, 4a,2…   35.3    24416     396212  22.0   102   11.0  4.50
## # ... with 10,116 more rows, and 24 more variables: maltene <dbl>,
## #   ref_amount_added.ug <dbl>, n_peaks <int>, n_standards <int>,
## #   ref_area.cpm <dbl>, amount.ug <dbl>, conc_rock.ug_g <dbl>,
## #   conc_tle.ug.g <dbl>, conc_maltene.ug.g <dbl>, calibration <chr>,
## #   data <list>, fit <list>, coefficients <list>, intercept <dbl>,
## #   intercept_se <dbl>, slope <dbl>, slope_se <dbl>, r2 <dbl>,
## #   total_volume.uL <dbl>, total_inject.uL <dbl>,
## #   ref_amount_inject_expected.ng <dbl>,
## #   ref_amount_inject_measured.ng <dbl>, ref_amount_measured.ug <dbl>,
## #   yield <dbl>

check yields

calib_data %>% 
  select(file_id, peak_name, yield)  %>% 
  arrange(file_id)  %>% 
  unique() %>% 
  ggplot() + aes(file_id, y = yield) +
  geom_point(size = 3) +
  theme_bw() + theme(axis.text.x = element_text(angle = 90, hjust = 0, vjust = 0.5))

Combine compounds/make ratios (new rows w/o RTs etc, just concentration.rock column)

# functions to make it easy to sum up peaks

sum_peaks <- function(df, filter_condition, new_peak_name) {
  filter_condition <- sprintf("(%s)", str_c(filter_condition, collapse = "|"))
  filter(df, str_detect(peak_name, filter_condition)) %>% 
    summarize(
      file_id = file_id[1],
      depth = depth[1],
      conc_tle.ug.g = sum(conc_tle.ug.g)
    ) %>% 
    mutate(peak_name = new_peak_name)
}

ratio_peaks <- function(df, filter_top, filter_bottom, new_peak_name) {
  filter_top <- sprintf("(%s)", str_c(filter_top, collapse = "|"))
  filter_bottom <- sprintf("(%s)", str_c(filter_bottom, collapse = "|"))
  filter(df, str_detect(peak_name, filter_top) | str_detect(peak_name, filter_bottom)) %>% 
    summarize(
      file_id = file_id[1],
      depth = depth[1],
      ratio = sum(conc_tle.ug.g[str_detect(peak_name, filter_top)]) / sum(conc_tle.ug.g[str_detect(peak_name, filter_bottom)])
    ) %>% 
    mutate(peak_name = new_peak_name)
}

#set values to use for later calculations
final_data1 <- calib_data %>% 
    group_by(file_id) %>% 
        do({
          bind_rows(., 
              #C27_Dia/Reg
                sum_peaks(.,  c("C27 aB 20R ST", "C27 aB 20S ST"), "C27Dia"),      
                sum_peaks(., c("C27 aaa 20R ST", "C27 aaa 20S ST", "C27 aBB 20R ST", "C27 aBB 20S ST", "C27 Ba 20R ST", "C27 Ba 20S ST"), "C27Reg"),
            
              #Total Tricyclics
                sum_peaks(., c("C19 Tri HO", "C20 Tri HO", "C21 Tri HO", "C22 Tri HO", "C23 Tri HO", "C24 Tet HO", "C24 Tri HO", "C25 Tri R HO", "C25 Tri S HO", "C26 Tri R HO", "C26 Tri S HO"), "all_tricyclics"),
            
              #4Me_TriMe
                sum_peaks(., c("4B Me 5a cholestane", "4B Me 24 ethyl 5a cholestane", "4B,23S,24S trimethyl 5a cholestane", "4B,23S,24R trimethyl 5a cholestane", "4B,23R,24S trimethyl 5a cholestane", "4B,23R,24R trimethyl 5a cholestane", "4a Me 5a cholestane", "4a Me 24 ethyl 5a cholestane", "4a,23S,24S trimethyl 5a cholestane", "4a,23S,24R trimethyl 5a cholestane", "4a,23R,24S trimethyl 5a cholestane", "4a,23R,24R trimethyl 5a cholestane"), "4Me_TriMe"),
            
              #allRegSt
                sum_peaks(., c("C26 aBB 20S ST", "C26 aBB 20R ST", "C26 aaa 20S ST", "C26 aaa 20R ST","C27 aBB 20S ST", "C27 aBB 20R ST", "C27 aaa 20S ST", "C27 aaa 20R ST", "C28 aBB 20S ST", "C28 aBB 20R ST", "C28 aaa 20S ST", "C28 aaa 20R ST","C29 aBB 20S ST", "C29 aBB 20R ST", "C29 aaa 20S ST", "C29 aaa 20R ST", "C30 aBB 20 R+S ST", "C30 aaa 20S ST", "C30 aaa 20R ST"), "allRegst"),
            
              #allRegHO
                sum_peaks(., c("Ts C27 HO", "Tm C27 HO", "C27 17B H Ho", "29, 30 C28H bisnor HO", "28, 30 C28 bisnor HO", "C29 Ts HO", "C29 Ba HO", "C29 BB Ho", "C30 aB HO", "C30 BB HO", "C30H Ba HO", "C31 HR Ba HO", "C31 aB HR HO", "C31 aB HS HO", "C31 BB HO", "C32 aB HS HO", "C32 aB HR HO", "C33 aB HS HO", "C33 aB HR HO", "C34 aB HR HO", "C34 aB HS HO", "C35 aB HR HO", "C35 aB HS HO"), "allRegHO") 
            
) }) %>% ungroup()

final_data <- final_data1 %>% 
    group_by(file_id) %>% 
        do({
          bind_rows(., 
            #Thermal Maturity
              #C27_Dia/Reg
                ratio_peaks(., "C27Dia", "C27Reg", "C27Dia/Reg"),
              #C27Dia_S/R
                ratio_peaks(., "C27 aB 20R ST", "C27 aB 20S ST", "C27Dia_S/R"),
              #C27Reg_abb/all 
                 ratio_peaks(., c("C27 aBB 20R ST", "C27 aBB 20S ST"), c("C27 aaa 20R ST", "C27 aaa 20S ST", "C27 aBB 20R ST", "C27 aBB 20S ST"), "C27Reg_abb/aaa"),
              #C27RegaaaS/S+R
                ratio_peaks(., "C27 aaa 20S ST", c("C27 aaa 20R ST", "C27 aaa 20S ST"), "C27Regaaa_S/S+R"), 
              #C27RegabbS/S+R
                ratio_peaks(., "C27 aBB 20S ST", c("C27 aBB 20S ST", "C27 aBB 20R ST"), "C27Regabb_S/S+R"),
              #C28Dia/all
                ratio_peaks(., c("C28 Ba 20S ST", "C28 Ba 20R ST"), c("C28 aBB 20S ST", "C28 aBB 20R ST", "C28 aaa 20S ST", "C28 aaa 20R ST", "C28 Ba 20S ST", "C28 Ba 20R ST"), "C28Dia/all"),
              #C28DiaS/S+R
                ratio_peaks(., "C28 Ba 20S ST", c("C28 Ba 20S ST", "C28 Ba 20R ST"), "C28DiaS/S+R"),
              #C28abb/all
                ratio_peaks(., c("C28 aBB 20S ST", "C28 aBB 20R ST"), c("C28 aBB 20S ST", "C28 aBB 20R ST", "C28 aaa 20S ST", "C28 aaa 20R ST"), "C28abb/all"),
              #C28aaaS/S+R
                ratio_peaks(., "C28 aaa 20S ST", c("C28 aaa 20S ST", "C28 aaa 20R ST"), "C28aaaS/S+R"),
              #C28abbS/S+R
                ratio_peaks(., "C28 aBB 20S ST", c("C28 aBB 20S ST", "C28 aBB 20R ST"), "C28abbS/S+R"),
              #C29Dia/all
                ratio_peaks(., c("C29 Ba 20S ST", "C29 Ba 20R ST"),  c("C29 Ba 20S ST", "C29 Ba 20R ST", "C29 aBB 20S ST", "C29 aBB 20R ST", "C29 aaa 20S ST", "C29 aaa 20R ST"), "C29Dia/all"),
              #C29DiaS/S+R
                ratio_peaks(., "C29 Ba 20S ST", c("C29 Ba 20S ST", "C29 Ba 20R ST"), "C29DiaS/S+R"),
              #C29abb/all
                ratio_peaks(., c("C29 aBB 20S ST", "C29 aBB 20R ST"), c( "C29 aaa 20S ST", "C29 aaa 20R ST", "C29 aBB 20S ST", "C29 aBB 20R ST" ), "C29abb/all"),
              #C29aaaS/S+R
                ratio_peaks(., "C29 aaa 20S ST", c("C29 aaa 20S ST", "C29 aaa 20R ST") , "C29aaaS/S+R"),
              #C29abbS/S+R
                ratio_peaks(., "C29 aBB 20S ST", c("C29 aBB 20S ST", "C29 aBB 20R ST"), "C29abbS/S+R"),
              #C27Ts/Ts+Tm
                ratio_peaks(., "Tm C27 HO", c("Ts C27 HO", "Tm C27 HO"), "C27Ts/Tm"),
              #C28BNH29,30/28,30
                ratio_peaks(., "29, 30 C28 bisnor HO", c("29, 30 C28 bisnor HO", "28, 30 C28 bisnor HO"), "C28BNH29,30/28,30"),
              #C29Ts/Ts+ab
                ratio_peaks(., "C29 Ts HO", c( "C29 aB HO", "C29 Ts HO"), "C29Ts/ab"),
              #C29ba/ba+ab
                ratio_peaks(.,"C29 Ba HO",  c("C29 aB HO", "C29 Ba HO"), "C29ba/ab"),
              #C29bb/bb+ab
                ratio_peaks(., "C29 BB Ho", c("C29 BB Ho", "C29 aB HO"), "C29bb/ab"),
              #C30_30nor/30nor+ab
                ratio_peaks(., "30-nor C30H HO", c("C30 aB HO", "30-nor C30H HO"),  "C30_30nor/ab"),
              #C30ba/ba+ab
                ratio_peaks(., "C30H Ba HO", c("C30 aB HO", "C30H Ba HO"), "C30ba/ab"),
              #C30bb/bb+ab
                ratio_peaks(., "C30 BB HO", c("C30 aB HO", "C30 BB HO"), "C30bb/ab"),
              #C31S/S+R
                ratio_peaks(., "C31 aB HS HO", c("C31 aB HR HO", "C31 aB HS HO"), "C31S/S+R"),
              #C32S/S+R
                ratio_peaks(., "C32 aB HS HO", c("C32 aB HS HO", "C32 aB HR HO"), "C32S/S+R"),
              #C33S/S+R
                ratio_peaks(., "C33 aB HS HO", c("C33 aB HS HO", "C33 aB HR HO"), "C33S/S+R"),
              #C34S/S+R
                ratio_peaks(., "C34 aB HS HO", c("C34 aB HS HO", "C34 aB HR HO") , "C34S/S+R"),
              #C35S/S+R
                ratio_peaks(., "C35 aB HS HO", c("C35 aB HS HO", "C35 aB HR HO") , "C35S/S+R"),
           #Source
              #C19/tricyclics
                ratio_peaks(., "C19 Tri HO", "all_tricyclics", "C19/tricyclics"),
              #C20/tricyclics
                ratio_peaks(., "C20 Tri HO", "all_tricyclics", "C20/tricyclics"),
              #C21/tricyclics
                ratio_peaks(., "C21 Tri HO", "all_tricyclics", "C21/tricyclics"),
              #C22/tricyclics
                ratio_peaks(., "C22 Tri HO", "all_tricyclics", "C22/tricyclics"),
              #C23/tricyclics
                ratio_peaks(., "C23 Tri HO", "all_tricyclics", "C23/tricyclics"),
              #C24/tricyclics
                ratio_peaks(., c("C24 Tet HO", "C24 Tri HO"), "all_tricyclics", "C24/tricyclics"),
              #C25/tricyclics
                ratio_peaks(., c("C25 Tri R HO", "C25 Tri S HO"), "all_tricyclics", "C25/tricyclics"),
              #C26/tricyclics
                ratio_peaks(., c("C26 Tri R HO", "C26 Tri S HO"), "all_tricyclics", "C26/tricyclics"),
              #tricyclics/all
                ratio_peaks(., "all_tricyclics", c(""), "tricyclics/all"),
              #C19/C19+23
                ratio_peaks(., "C19 Tri HO", c("C19 Tri HO", "C23 Tri HO"), "C19/C19+23"),
              #C20/C20+23
                ratio_peaks(., "C20 Tri HO", c("C20 Tri HO", "C23 Tri HO"), "C20/C20+23"),
           
              #C26St/allSt ##INCLUDES ME's
                ratio_peaks(., c("C26 Ba 20S ST", "C26 Ba 20R ST", "C26 aBB 20S ST", "C26 aBB 20R ST", "C26 aaa 20S ST", "C26 aaa 20R ST"), c("cholestane", "ST"), "C26St/allSt"), 
              #C27St/allSt
                ratio_peaks(., c("C27 aaa 20R ST", "C27 aaa 20S ST", "C27 aBB 20R ST", "C27 aBB 20S ST", "C27 Ba 20R ST", "C27 Ba 20S ST"), c("cholestane", "ST"), "C27St/allSt"),
              #C28St/allSt
                ratio_peaks(., c("C28 Ba 20S ST", "C28 Ba 20R ST", "C28 aBB 20S ST", "C28 aBB 20R ST", "C28 aaa 20S ST", "C28 aaa 20R ST"), c("cholestane", "ST"), "C28St/allSt"),
              #C29St/allSt
                ratio_peaks(., c("C29 Ba 20S ST", "C29 Ba 20R ST", "C29 aBB 20S ST", "C29 aBB 20R ST", "C29 aaa 20S ST", "C29 aaa 20R ST"), c("cholestane", "ST"), "C29St/allSt"),
              #C30St/allSt (does not include Me's in numerator)
                ratio_peaks(., c("C30 Ba 20S ST", "C30 Ba 20R ST", "C30 aBB 20(R+S) ST", "C30 aaa 20S ST", "C30 aaa 20R ST"), c("cholestane", "ST"), "C30St/allSt"),
              #C30Me/allSt (C30 Me's in numerator)(not in MRM spreadsheet)
                ratio_peaks(., c("C30 4a Me 20S ST", "C30 4a Me 20R ST + DINO st", "C30 3B Me BB 20S ST", "C30 3B Me BB 20R ST", "C30 3B Me 20S ST", "C30 3BMe 20R ST", "C30 2aMe 20S ST", "C30 2a Me 20R + 4a Me BB 20S ST"), c("cholestane", "ST"), "C30Me/allSt"),
              #DinoSt/allSt
                ratio_peaks(., c("4B Me 5a cholestane", "4B Me 24 ethyl 5a cholestane", "4B,23S,24S trimethyl 5a cholestane", "4B,23S,24R trimethyl 5a cholestane", "4B,23R,24S trimethyl 5a cholestane", "4B,23R,24R trimethyl 5a cholestane", "4a Me 5a cholestane", "4a Me 24 ethyl 5a cholestane", "4a,23S,24S trimethyl 5a cholestane", "4a,23S,24R trimethyl 5a cholestane", "4a,23R,24S trimethyl 5a cholestane", "4a,23R,24R trimethyl 5a cholestane"), c("cholestane", "ST"), "DinoSt/allSt"),
           
              #C26/(C26-30)aaaSR
                ratio_peaks(., c("C26 aaa 20R ST", "C26 aaa 20S ST"), c("aaa 20R ST", "aaa 20S ST") , "C26/(C26-30)aaaSR"),
              #C27/(C26-30)aaaSR
                ratio_peaks(., c("C27 aaa 20R ST", "C27 aaa 20S ST"), c("aaa 20R ST", "aaa 20S ST") , "C27/(C26-30)aaaSR"),
              #C28/(C26-30)aaaSR
                ratio_peaks(., c("C28 aaa 20R ST", "C28 aaa 20S ST"), c("aaa 20R ST", "aaa 20S ST") , "C28/(C26-30)aaaSR"),
              #C29/(C26-30)aaaSR
                ratio_peaks(., c("C29 aaa 20R ST", "C29 aaa 20S ST"), c("aaa 20R ST", "aaa 20S ST") , "C29/(C26-30)aaaSR"),
              #C30/(C26-30)aaaSR
                ratio_peaks(., c("C30 aaa 20R ST", "C30 aaa 20S ST"), c("aaa 20R ST", "aaa 20S ST") , "C30/(C26-30)aaaSR"),
           
              #C27/C27+C28aaa&abb
                ratio_peaks(., c("C27 aaa 20R ST" , "C27 aaa 20S ST", "C27 aBB 20R ST", "C27 aBB 20S ST"), c("C27 aaa 20R ST" , "C27 aaa 20S ST", "C27 aBB 20R ST", "C27 aBB 20S ST", "C28 aaa 20R ST", "C28 aaa 20S ST", "C28 aBB 20R ST", "C28 aBB 20S ST")  , "C27/C27+C28aaa&abb"),
              #C27/C27+C29aaa&abb
                ratio_peaks(., c("C27 aaa 20R ST" , "C27 aaa 20S ST", "C27 aBB 20R ST", "C27 aBB 20S ST"), c("C27 aaa 20R ST" , "C27 aaa 20S ST", "C27 aBB 20R ST", "C27 aBB 20S ST", "C29 aaa 20R ST", "C29 aaa 20S ST", "C29 aBB 20R ST", "C29 aBB 20S ST")  , "C27/C27+C29aaa&abb"),
              #C28/C28+C27aaa&abb
                ratio_peaks(., c("C28 aaa 20R ST", "C28 aaa 20S ST", "C28 aBB 20R ST", "C28 aBB 20S ST"), c("C27 aaa 20R ST" , "C27 aaa 20S ST", "C27 aBB 20R ST", "C27 aBB 20S ST", "C28 aaa 20R ST", "C28 aaa 20S ST", "C28 aBB 20R ST", "C28 aBB 20S ST")  , "C28/C28+C27aaa&abb"),
              #C28/C28+C29aaa&abb
                ratio_peaks(., c("C28 aaa 20R ST", "C28 aaa 20S ST", "C28 aBB 20R ST", "C28 aBB 20S ST"), c("C29 aaa 20R ST", "C29 aaa 20S ST", "C29 aBB 20R ST", "C29 aBB 20S ST", "C28 aaa 20R ST", "C28 aaa 20S ST", "C28 aBB 20R ST", "C28 aBB 20S ST")  , "C28/C28+C29aaa&abb"),
              #C29/C29+C27aaa&abb
                ratio_peaks(., c("C29 aaa 20R ST", "C29 aaa 20S ST", "C29 aBB 20R ST", "C29 aBB 20S ST"), c("C27 aaa 20R ST" , "C27 aaa 20S ST", "C27 aBB 20R ST", "C27 aBB 20S ST", "C29 aaa 20R ST", "C29 aaa 20S ST", "C29 aBB 20R ST", "C29 aBB 20S ST")  , "C29/C29+C27aaa&abb"),
              #C29/C29+C28aaa&abb
                ratio_peaks(., c("C29 aaa 20R ST", "C29 aaa 20S ST", "C29 aBB 20R ST", "C29 aBB 20S ST"), c("C29 aaa 20R ST", "C29 aaa 20S ST", "C29 aBB 20R ST", "C29 aBB 20S ST", "C28 aaa 20R ST", "C28 aaa 20S ST", "C28 aBB 20R ST", "C28 aBB 20S ST")  , "C29/C29+C28aaa&abb"),
              
              #4Me_TriMe/Me_C26St
                ratio_peaks(., c("4Me_TriMe"), c("4Me_TriMe", "C26 aBB 20S ST", "C26 aBB 20R ST", "C26 aaa 20S ST", "C26 aaa 20R ST") , "4Me_TriMe/Me_C26St"),
              #4Me_TriMe/Me_C27St
                ratio_peaks(., c("4Me_TriMe"), c("4Me_TriMe", "C27 aBB 20S ST", "C27 aBB 20R ST", "C27 aaa 20S ST", "C27 aaa 20R ST") , "4Me_TriMe/Me_C27St"),
              #4Me_TriMe/Me_C28St
                ratio_peaks(., c("4Me_TriMe"), c("4Me_TriMe", "C28 aBB 20S ST", "C28 aBB 20R ST", "C28 aaa 20S ST", "C28 aaa 20R ST") , "4Me_TriMe/Me_C28St"),
              #4Me_TriMe/Me_C29St
                ratio_peaks(., c("4Me_TriMe"), c("4Me_TriMe", "C29 aBB 20S ST", "C29 aBB 20R ST", "C29 aaa 20S ST", "C29 aaa 20R ST") , "4Me_TriMe/Me_C29St"),
              #4Me_TriMe/Me_C30St
                ratio_peaks(., c("4Me_TriMe"), c("4Me_TriMe", "C30 aBB 20 R+S ST", "C30 aaa 20S ST", "C30 aaa 20R ST") , "4Me_TriMe/Me_C30St"),
              #4Me_TriMe/Me_allSt
                ratio_peaks(., c("4Me_TriMe"), c("4Me_TriMe", "allRegst") , "4Me_TriMe/Me_allSt"),
           
              #C26-30St/C26-C30St+regHo ###missing some
                ratio_peaks(., c("allRegst"), c("allRegst", "Ts C27 HO", "Tm C27 HO", "C27 17B HO", "29, 30 C28 bisnor HO", "28, 30 C28 bisnor HO", "C29 Ts HO", "C29 Ba HO", "C29 BB Ho", "C30 aB HO", "C30 BB HO", "C30H Ba HO", "C31 HR Ba HO", "C31 aB HR HO", "C31 aB HS HO", "C31 BB HO", "C32 aB HS HO", "C32 aB HR HO", "C33 aB HS HO", "C33 aB HR HO", "C34 aB HR HO", "C34 aB HS HO", "C35 aB HR HO", "C35 aB HS HO"), "C26-30St/C26-C30St_regHo"),
              #C27-C30aaaSt/C27-C30aaaSt+regHo
                ratio_peaks(., c( "C26 aaa 20S ST", "C26 aaa 20R ST", "C27 aaa 20S ST", "C27 aaa 20R ST", "C28 aaa 20S ST", "C28 aaa 20R ST", "C29 aaa 20S ST", "C29 aaa 20R ST", "C30 aaa 20S ST", "C30 aaa 20R ST"), c("C26 aaa 20S ST", "C26 aaa 20R ST", "C27 aaa 20S ST", "C27 aaa 20R ST", "C28 aaa 20S ST", "C28 aaa 20R ST", "C29 aaa 20S ST", "C29 aaa 20R ST", "C30 aaa 20S ST", "C30 aaa 20R ST", "allRegHO"), "C27-C30aaaSt/C27-C30aaaSt+regHo"),
              #Ho/St
                ratio_peaks(., "allRegHO", c("C26 aaa 20S ST", "C26 aaa 20R ST", "C27 aaa 20S ST", "C27 aaa 20R ST", "C28 aaa 20S ST", "C28 aaa 20R ST", "C29 aaa 20S ST", "C29 aaa 20R ST", "C30 aaa 20S ST", "C30 aaa 20R ST"), "Ho/St"),
              #Ho/St%
                ratio_peaks(., "allRegHO", c("C26 aaa 20S ST", "C26 aaa 20R ST", "C27 aaa 20S ST", "C27 aaa 20R ST", "C28 aaa 20S ST", "C28 aaa 20R ST", "C29 aaa 20S ST", "C29 aaa 20R ST", "C30 aaa 20S ST", "C30 aaa 20R ST", "allRegHO" ), "Ho/St%"),
            
              #C31_2MHI
                ratio_peaks(., "C31 2a Me Ho", c("C30 aB HO", "C31 2a Me Ho" ), "C31_2MHI"),
              #C31_35_2MHI
                ratio_peaks(., c("C31 2a Me Ho", "C32 2aMe R HO", "C32 2aMe S HO", "C33 2aMe S HO", "C33 2aMe R HO", "C34 2a Me S HO", "C34 2a Me R HO", "C36 2a Me R HO", "C36 2a Me S HO"), c("C30 aB HO", "C31 2a Me Ho", "C32 2aMe R HO", "C32 2aMe S HO", "C33 2aMe S HO", "C33 2aMe R HO", "C34 2a Me S HO", "C34 2a Me R HO", "C36 2a Me R HO", "C36 2a Me S HO"), "C31_35_2MHI"),
              #C31_2-MHI/C27-C30Steranes
                ratio_peaks(., "C31 2a Me Ho", c("C26 aaa 20S ST", "C26 aaa 20R ST", "C27 aaa 20S ST", "C27 aaa 20R ST" ,"C28 aaa 20S ST", "C28 aaa 20R ST", "C29 aaa 20S ST", "C29 aaa 20R ST", "C30 aaa 20S ST", "C30 aaa 20R ST", "C31 2a Me Ho" ), "C31_2-MHI/C27-C30Steranes"),
              #C31 3-MHI 
                ratio_peaks(., "C31 3B Me HO", c("C31 3B Me HO", "C30 aB HO"), "C31 3-MHI"), 
              #C31_35_3MHI_percent
                 ratio_peaks(., c("C31 3B Me HO", "C32 3B Me S HO", "C32 3B Me R HO", "C32 3B Me Ba 22S+R ST", "C33 3BMe S HO", "   
C33 3BMe R HO", "C34 3B Me S Ho", "C34 3B Me R HO", "C35 3B Me R HO", "C35 3B Me S HO", "C36 3B Me S HO", "C36 3B Me R HO"), c("C30 aB HO","C31 3B Me HO", "C32 3B Me S HO", "C32 3B Me R HO", "C32 3B Me Ba 22S+R ST", "C33 3BMe S HO", "C33 3BMe R HO", "C34 3B Me S HO", "C34 3B Me R HO", "C35 3B Me R HO", "C35 3B Me S HO", "C36 3B Me S HO", "C36 3B Me R HO" ) ,"C31_35_3MHI_percent"),

              #C29ab/C29ab+C30ab
                 ratio_peaks(., "C29 aB HO", c( "C29 aB HO" , "C30 aB HO"), "C29ab/C29ab+C30ab"), 
              #C29ab/allHoab
                 ratio_peaks(., "C29 aB HO" , c("C35 aB HS HO", "C35 aB HR HO", "C34 aB HS HO", "C34 aB HR HO", "C33 aB HS HO" , "C33 aB HR HO", "C32 aB HR HO", "C32 aB HS HO", "C31 aB HS HO", "C31 aB HR HO", "C30 aB HO", "C29 aB HO"), "C29ab/allHoab"), 
              #C30ab/allHoab 
                 ratio_peaks(., "C30 aB HO" , c("C35 aB HS HO", "C35 aB HR HO", "C34 aB HS HO", "C34 aB HR HO", "C33 aB HS HO" , "C33 aB HR HO", "C32 aB HR HO", "C32 aB HS HO", "C31 aB HS HO", "C31 aB HR HO", "C30 aB HO", "C29 aB HO"), "C30ab/allHoab"), 
              #C31ab/allHoab 
                 ratio_peaks(., c("C31 aB HS HO", "C31 aB HR HO") , c("C35 aB HS HO", "C35 aB HR HO", "C34 aB HS HO", "C34 aB HR HO", "C33 aB HS HO" , "C33 aB HR HO", "C32 aB HR HO", "C32 aB HS HO", "C31 aB HS HO", "C31 aB HR HO", "C30 aB HO", "C29 aB HO"), "C31ab/allHoab"),
              #C32ab/allHoab 
                 ratio_peaks(., c("C32 aB HR HO", "C32 aB HS HO") , c("C35 aB HS HO", "C35 aB HR HO", "C34 aB HS HO", "C34 aB HR HO", "C33 aB HS HO" , "C33 aB HR HO", "C32 aB HR HO", "C32 aB HS HO", "C31 aB HS HO", "C31 aB HR HO", "C30 aB HO", "C29 aB HO"), "C32ab/allHoab"),
              #C33ab/allHoab 
                 ratio_peaks(., c( "C33 aB HS HO" , "C33 aB HR HO") , c("C35 aB HS HO", "C35 aB HR HO", "C34 aB HS HO", "C34 aB HR HO", "C33 aB HS HO" , "C33 aB HR HO", "C32 aB HR HO", "C32 aB HS HO", "C31 aB HS HO", "C31 aB HR HO", "C30 aB HO", "C29 aB HO"), "C33ab/allHoab"),
              #C34ab/allHoab 
                 ratio_peaks(., c( "C34 aB HS HO", "C34 aB HR HO") , c("C35 aB HS HO", "C35 aB HR HO", "C34 aB HS HO", "C34 aB HR HO", "C33 aB HS HO" , "C33 aB HR HO", "C32 aB HR HO", "C32 aB HS HO", "C31 aB HS HO", "C31 aB HR HO", "C30 aB HO", "C29 aB HO"), "C34ab/allHoab"),
              #C35ab/allHoab 
                 ratio_peaks(., c("C35 aB HS HO", "C35 aB HR HO") , c("C35 aB HS HO", "C35 aB HR HO", "C34 aB HS HO", "C34 aB HR HO", "C33 aB HS HO" , "C33 aB HR HO", "C32 aB HR HO", "C32 aB HS HO", "C31 aB HS HO", "C31 aB HR HO", "C30 aB HO", "C29 aB HO"), "C35ab/allHoab"),
              #OleananeIndex
                ratio_peaks(., "Oleanane HO", c("Oleanane HO", "C30 aB HO"), "OleananeIndex"),

            #Source
              #HHI
                ratio_peaks(., c("C35 aB HS HO", "C35 aB HR HO") , c("C35 aB HS HO", "C35 aB HR HO", "C34 aB HS HO", "C34 aB HR HO", "C33 aB HS HO" , "C33 aB HR HO", "C32 aB HR HO", "C32 aB HS HO", "C31 aB HS HO", "C31 aB HR HO"), "HHI"),
              #C35/C35+C34
                ratio_peaks(., c("C35 aB HS HO", "C35 aB HR HO"), c("C34 aB HS HO", "C34 aB HR HO","C35 aB HS HO", "C35 aB HR HO"), "C35/C35+C34"),
              #GI
                ratio_peaks(., "gamma", c("gamma", "C30 aB HO"), "GI"),
              #28,30BNH/28,30BNH+C30
                ratio_peaks(., "28, 30 C28 bisnor HO", c("28, 30 C28 bisnor HO", "C30 aB HO"), "28,30BNH/28,30BNH+C30")
              
 ) }) %>% ungroup() 
  
final_data

## # A tibble: 16,763 x 34
##    file_id  peak_name  RT.min area.cpm height.cts    OG depth rock.g   tle
##    <chr>    <chr>       <dbl>    <dbl>      <dbl> <dbl> <dbl>  <dbl> <dbl>
##  1 TSQ3466… 20R 4a,24…   34.7    44365     400048  22.0   102   11.0  4.50
##  2 TSQ3466… 20R, 4a M…   33.4    33268     424790  22.0   102   11.0  4.50
##  3 TSQ3466… 20R, 4a M…   32.8    48349     759077  22.0   102   11.0  4.50
##  4 TSQ3466… 20S, 4a M…   32.1    48728     879884  22.0   102   11.0  4.50
##  5 TSQ3466… 20S, 4a,2…   35.8    30909     259440  22.0   102   11.0  4.50
##  6 TSQ3466… 20S, 4a,2…   34.0    46342     445181  22.0   102   11.0  4.50
##  7 TSQ3466… 25-nor C2…   37.6    11915     155542  22.0   102   11.0  4.50
##  8 TSQ3466… 28, 30 C2…   37.0    27634     343969  22.0   102   11.0  4.50
##  9 TSQ3466… 29, 30 C2…   35.8     5411      63017  22.0   102   11.0  4.50
## 10 TSQ3466… 2RS, 4a,2…   35.3    24416     396212  22.0   102   11.0  4.50
## # ... with 16,753 more rows, and 25 more variables: maltene <dbl>,
## #   ref_amount_added.ug <dbl>, n_peaks <int>, n_standards <int>,
## #   ref_area.cpm <dbl>, amount.ug <dbl>, conc_rock.ug_g <dbl>,
## #   conc_tle.ug.g <dbl>, conc_maltene.ug.g <dbl>, calibration <chr>,
## #   data <list>, fit <list>, coefficients <list>, intercept <dbl>,
## #   intercept_se <dbl>, slope <dbl>, slope_se <dbl>, r2 <dbl>,
## #   total_volume.uL <dbl>, total_inject.uL <dbl>,
## #   ref_amount_inject_expected.ng <dbl>,
## #   ref_amount_inject_measured.ng <dbl>, ref_amount_measured.ug <dbl>,
## #   yield <dbl>, ratio <dbl>

Against depth

D4

subset(final_data, peak_name=="D4 C29 ISTD") %>% 
    ggplot() +
    aes(x = amount.ug, y = depth) +
    geom_point() +
    facet_wrap(~peak_name, scales = "free") +
    scale_y_reverse() 

## Warning: Removed 3 rows containing missing values (geom_point).

ratios etc

subset(final_data, peak_name== "C27Dia/Reg") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "C27Dia_S/R") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 6 rows containing missing values (geom_point).

subset(final_data, peak_name== "C27Reg_abb/aaa") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "C27Regaaa_S/S+R") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "C27Regabb_S/S+R") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "C28Dia/all") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "C28DiaS/S+R") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 5 rows containing missing values (geom_point).

subset(final_data, peak_name== "C28abb/all") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 5 rows containing missing values (geom_point).

subset(final_data, peak_name== "C28aaaS/S+R") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 5 rows containing missing values (geom_point).

subset(final_data, peak_name== "C28abbS/S+R") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 5 rows containing missing values (geom_point).

subset(final_data, peak_name== "C29Dia/all") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "C29DiaS/S+R") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 5 rows containing missing values (geom_point).

subset(final_data, peak_name== "C29abb/all") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "C29aaaS/S+R") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "C29abbS/S+R") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "C27Ts/Tm") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 8 rows containing missing values (geom_point).

subset(final_data, peak_name== "C28BNH29,30/28,30") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 7 rows containing missing values (geom_point).

subset(final_data, peak_name== "C29Ts/ab") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "C29ba/ab") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 3 rows containing missing values (geom_point).

subset(final_data, peak_name== "C29bb/ab") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "C30_30nor/ab") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "C30ba/ab") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 3 rows containing missing values (geom_point).

subset(final_data, peak_name== "C30bb/ab") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 3 rows containing missing values (geom_point).

subset(final_data, peak_name== "C31S/S+R") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 5 rows containing missing values (geom_point).

subset(final_data, peak_name== "C32S/S+R") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "C33S/S+R") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "C34S/S+R") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 6 rows containing missing values (geom_point).

subset(final_data, peak_name== "C35S/S+R") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "C19/tricyclics") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "C20/tricyclics") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "C21/tricyclics") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "C22/tricyclics") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "C23/tricyclics") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "C24/tricyclics") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "C25/tricyclics") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "C26/tricyclics") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "tricyclics/all") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "C19/C19+23") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 6 rows containing missing values (geom_point).

subset(final_data, peak_name== "C20/C20+23") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 5 rows containing missing values (geom_point).

subset(final_data, peak_name== "C26St/allSt") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "C27St/allSt") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "C28St/allSt") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "C29St/allSt") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "C30St/allSt") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "C30Me/allSt") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "DinoSt/allSt") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "C26/(C26-30)aaaSR") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "C27/(C26-30)aaaSR") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "C28/(C26-30)aaaSR") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "C29/(C26-30)aaaSR") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "C30/(C26-30)aaaSR") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "C27/C27+C28aaa&abb") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "C27/C27+C29aaa&abb") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "C28/C28+C27aaa&abb") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "C28/C28+C29aaa&abb") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "C29/C29+C27aaa&abb") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "C29/C29+C28aaa&abb") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "4Me_TriMe/Me_C26St") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "4Me_TriMe/Me_C27St") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "4Me_TriMe/Me_C28St") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "4Me_TriMe/Me_C29St") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "4Me_TriMe/Me_C30St") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "4Me_TriMe/Me_allSt") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "C26-30St/C26-C30St_regHo") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "C27-C30aaaSt/C27-C30aaaSt+regHo") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "Ho/St") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "C31_2MHI") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 3 rows containing missing values (geom_point).

subset(final_data, peak_name== "C31_35_2MHI") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "C31_2-MHI/C27-C30Steranes") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "C31 3-MHI") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "C31_35_3MHI_percent") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "C29ab/C29ab+C30ab") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "C29ab/allHoab") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "C30ab/allHoab") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "C31ab/allHoab") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "C32ab/allHoab") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "C33ab/allHoab") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "C34ab/allHoab") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "C35ab/allHoab") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "OleananeIndex") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "HHI") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "C35/C35+C34") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "GI") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).

subset(final_data, peak_name== "28,30BNH/28,30BNH+C30") %>%
  ggplot() +
  aes(x = ratio, y = depth) +
  geom_point() +
  facet_wrap(~peak_name, scales = "free") +
  scale_y_reverse()

## Warning: Removed 4 rows containing missing values (geom_point).